Contacts of the helix formed by residues 334 - 347 (chain B) in PDB entry 1P5Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 334 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329B HIS* 2.9 34.4 + - - +
332B LEU* 4.2 10.5 - - + +
333B GLN* 1.3 74.9 - - - +
335B PHE* 1.3 58.5 - - - +
336B SER 3.4 2.9 - - - -
337B ALA* 3.1 10.0 + - + -
338B ALA 3.0 22.2 + - - -
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Residues in contact with PHE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B LEU* 3.6 32.5 - - + -
333B GLN* 3.3 49.0 + - + -
334B ALA* 1.3 72.6 - - - +
336B SER* 1.3 60.6 + - - +
338B ALA* 3.2 5.1 + - - +
339B ILE* 2.9 34.6 + - + +
362B ALA* 3.8 5.2 - - + +
365B ALA* 3.4 29.8 - - + -
366B VAL* 3.4 32.3 - - + -
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Residues in contact with SER 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B ALA 3.4 0.8 - - - -
335B PHE* 1.3 77.4 - - - +
337B ALA* 1.3 62.2 + - - +
339B ILE* 3.4 12.3 + - - +
340B GLU* 3.0 23.2 + - - +
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B HIS* 3.5 29.8 - - + +
334B ALA* 3.1 15.9 + - + +
336B SER* 1.3 79.1 - - - +
338B ALA* 1.3 58.5 + - - +
340B GLU* 3.2 8.1 + - - +
341B SER* 2.8 32.6 + - - -
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B ALA* 4.1 6.1 - - + +
329B HIS* 3.5 22.6 - - + +
330B LEU* 3.5 36.6 - - + +
334B ALA 3.0 9.5 + - - +
335B PHE 3.2 7.4 + - - +
337B ALA* 1.3 73.6 - - - +
339B ILE* 1.3 65.8 + - - +
341B SER* 3.1 4.7 + - - +
342B CYS* 3.0 29.0 + - - -
358B ARG 5.6 0.4 - - - +
362B ALA* 4.2 2.9 - - + -
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B PHE* 2.9 20.4 + - + +
336B SER* 3.6 12.3 - - - +
338B ALA* 1.3 75.1 - - - +
340B GLU* 1.3 66.3 + - - +
342B CYS* 3.2 4.9 + - - +
343B ASN* 3.1 35.7 + - - +
359B ARG* 4.0 17.5 - - + -
362B ALA* 3.9 14.8 - - + +
363B HIS* 3.2 48.2 - - + +
366B VAL* 5.6 6.5 - - + -
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B SER 3.0 18.7 + - - +
337B ALA* 3.3 9.6 - - - +
338B ALA 3.1 0.2 - - - -
339B ILE* 1.3 80.1 - - - +
341B SER* 1.3 61.5 + - - +
342B CYS 3.2 0.7 + - - -
343B ASN* 3.3 19.7 + - - +
344B LYS* 2.5 69.4 + - - +
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B HIS* 3.4 35.9 + - - +
325B LEU* 3.8 13.1 - - - +
326B ALA* 4.0 12.6 - - - -
329B HIS* 3.7 13.8 + - - -
337B ALA 2.8 20.0 + - - -
338B ALA 3.1 4.5 + - - -
340B GLU* 1.3 70.3 - - - +
342B CYS* 1.3 64.8 + - - +
344B LYS* 3.6 7.5 + - - +
345B ALA* 3.4 14.0 + - - +
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Residues in contact with CYS 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B LEU* 5.6 0.9 - - - -
326B ALA* 4.1 10.5 - - - -
338B ALA* 3.0 16.0 + - - -
339B ILE 3.4 9.2 - - - +
340B GLU 3.1 0.2 - - - -
341B SER* 1.3 77.3 - - - +
343B ASN* 1.3 58.4 + - - +
344B LYS 3.1 0.2 - - - -
345B ALA* 2.7 26.2 + - - +
346B LEU* 2.9 18.1 + - + +
355B GLY* 3.2 17.7 - - - +
358B ARG* 3.8 13.2 - - - -
359B ARG* 3.2 47.3 - - + -
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Residues in contact with ASN 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B ILE* 3.1 21.1 + - - +
340B GLU* 3.3 26.4 + - - +
342B CYS* 1.3 76.9 - - - +
344B LYS* 1.3 60.0 + - - +
346B LEU* 3.3 6.6 + - - +
347B GLU* 2.9 38.5 + - - +
359B ARG* 2.8 37.7 + - - -
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Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B HIS* 3.2 47.3 - - + +
340B GLU* 2.5 70.7 + - - +
341B SER* 4.1 2.9 - - - +
342B CYS 3.1 1.0 - - - -
343B ASN* 1.3 81.5 - - - +
345B ALA* 1.3 60.2 + - - +
347B GLU* 4.0 23.4 + - - +
348B LEU* 3.6 13.9 - - - +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B LEU* 3.7 17.8 - - + +
322B HIS* 4.0 9.6 - - + -
323B LEU* 3.4 34.8 - - + -
341B SER 3.4 11.2 + - - +
342B CYS* 2.7 11.5 + - - +
344B LYS* 1.3 75.4 - - - +
346B LEU* 1.3 56.5 + - + +
347B GLU 3.1 0.9 - - - -
348B LEU* 2.7 29.7 + - - +
349B ASP 3.2 8.3 + - - -
352B ASN* 5.1 0.7 - - - +
355B GLY* 4.9 2.5 - - - -
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B CYS 2.9 17.7 + - - +
343B ASN* 3.9 5.8 - - - +
345B ALA* 1.3 76.5 - - - +
347B GLU* 1.3 62.3 + - - +
349B ASP 3.6 15.9 - - - +
350B SER* 3.0 35.6 + - - +
352B ASN* 4.1 7.2 - - + -
355B GLY* 3.9 10.5 - - - -
356B LEU* 3.3 52.7 - - + +
359B ARG* 3.4 33.0 - - - +
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B ASN* 2.9 26.0 + - - +
344B LYS* 4.1 26.2 - - - +
345B ALA 3.0 0.4 + - - -
346B LEU* 1.3 76.2 - - - +
348B LEU* 1.3 67.0 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il